Here are the steps I took:
1) I generated a testbench in Qsys with Generate>Generate Testbench System.
2) I then generated my HDL with Generate>Generate HDL>"Create simulation model == Verilog". This produces a folder {project directory}/{system fileneame}/simulation/
3) In modelsim, I created a new project, added the toplevel file in the /simulaton/ folder
4) In modelsim, I tried File>Load>Marco File>{./simulation/mentor/msim_setup.tcl}
5) Nothing happens, so I run dev_com and com.
6) Recieve error:
# ** Error: (vlog-7) Failed to open design unit file "./..//submodules/verbosity_pkg.sv" in read mode.
# C:/intelFPGA/16.1/modelsim_ase/win32aloem/vlog failed.
# Load canceled
# Load canceled
7) Check for spaces in pathnames. There are none.
8) Tried to set up my own simulaton with. Simulate>Start Simulation>work>{toplevel file.v}. Also loaded all libraries that were compiled in the compile tab. The results are produced below:
# vsim -gui -Lf altera_mf_ver work.single_sys_path -L work -L altera_common_sv_packages -L avalon_st_adapter -L avalon_st_adapter_001 -L c2 -L clock_mod -L clock_source -L demux -L discard_sink -L error_adapter_0 -L fe -L final_buff_ovf -L ip6_buff_ovf -L mt6d_process_path -L mt6d_srt -L mux -L pa -L packet_gen -L reset_source -L srt_dp_bwc
# Start time: 18:55:49 on Mar 02,2017
# Loading work.single_sys_path
# ** Error: (vsim-3033) C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/single_sys_path.v(55): Instantiation of 'clock_mod' failed. The design unit was not found.
# Time: 0 ps Iteration: 0 Instance: /single_sys_path File: C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/single_sys_path.v
# Searched libraries:
# C:/intelFPGA/16.1/modelsim_ase/altera/verilog/altera_mf
# C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/libraries/work
# C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/libraries/altera_common_sv_packages
# C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/libraries/avalon_st_adapter
# C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/libraries/avalon_st_adapter_001
# C:/Users/Joseph/Documents/local_repos/he_mt6d/single_sys_path/simulation/libraries/c2
{continues to list all libraries.}
... and basically for every module thereafter repeats this error